Aside from Soundflower, I’d highly suggest Rogue Amoeba’s Loopback Audio, when on Mac. It essentially does the same thing, but unlike soundflower, it continues working after each Mac OSX update. Loopback costs around $20 I think, but it has proven a lot more stable.
Combine loopback with rogue amoeba’s other offering (Audio Hijack), and you can create multiple audio stages in a pipeline with delay artificially induced. That way if the audio reactivity in MM has a 50ms delay, you can then delay the final audio output by 50ms (delaying just what you hear, not what MM hears) to get things perfectly in sync.
This works great for other audio-reactive viz software too. Even with small audio buffers there will always be a lag.
I pipe audio from Ableton Live (as well as Djay Pro & Traktor) through Loopback Audio so that MM can read the audio spectrum, but also use Ableton Link to get the beats aligned. It sounds like you want to avoid sending MIDI signals from Live — have you considered OSC? If you have Live Suite, I can send you a M4L patch specific to MM to do basic things like trigger cues in row X + column Y, if that would be helpful. Then you can automate those alongside your audio file (the patch uses OSC).